Opening Mechanism of G·T/U Pairs in DNA and RNA Duplexes: A Combined Study of Imino Proton Exchange and Molecular Dynamics Simulation
- 14 October 2004
- journal article
- research article
- Published by American Chemical Society (ACS) in Journal of the American Chemical Society
- Vol. 126 (44) , 14659-14667
- https://doi.org/10.1021/ja0470721
Abstract
The opening pathway of wobble pairs dG·T and rG·U has been investigated in four DNA and two RNA duplexes. Using NMR spectroscopy, we measured the imino proton exchange of both G(H1) and T/U(H3), catalyzed by ammonia, tris, and OH-, and we calculated the free energy surface related to G·T/U opening by molecular dynamics simulations. Taken together the experimental and theoretical results, we suggest that wobble pairs open through a coupled rotation of the bases toward the major groove where exchange of both imino protons takes place with the surrounding water.Keywords
This publication has 21 references indexed in Scilit:
- Nucleic Acid Base Pair Dynamics: The Impact of Sequence and Structure Using Free-Energy CalculationsJournal of the American Chemical Society, 2003
- Base Flipping in DNA: Pathways and Energetics Studied with Molecular Dynamic SimulationsJournal of the American Chemical Society, 2002
- Free Energy and Structural Pathways of Base Flipping in a DNA GCGC Containing SequenceJournal of Molecular Biology, 2002
- Imino Proton Exchange and Base-Pair Kinetics in RNA DuplexesBiochemistry, 2001
- How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?Journal of Computational Chemistry, 2000
- Observation of Spontaneous Base Pair Breathing Events in the Molecular Dynamics Simulation of a Difluorotoluene-Containing DNA OligonucleotideJournal of the American Chemical Society, 1999
- Constant-temperature free energy surfaces for physical and chemical processesThe Journal of Physical Chemistry, 1993
- THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The methodJournal of Computational Chemistry, 1992
- Lateral interactions of pig apolipoprotein A-1 with egg yolk phosphatidylcholine and with cholesterol in mixed monolayers at the triolein-saline interfaceBiochemistry, 1992
- Processes of base-pair opening and proton exchange in Z-DNABiochemistry, 1990